* bump example notebooks branch
* add ipykernel to env
* roll back to fixing septop branch
* i dont think we want ipykernel
* bump to tmp_fix_docs branch
* point to branch revert-237-v1.7_cookbooks
* point to latest example notebooks release
* fix nb link
* bump examplenotebooks version
* add dark mode option back in
* temporary pin to working ofe theme branch
* remove unused code
* bump ci
* bump ofe-sphinx-theme pin
* try mambaforge build
* Revert "try mambaforge build"
This reverts commit 683e07f1ea.
* try explicit build
* try removing ambertools
* use the right env
* just add gufe pip install back
* add back openfe eco packages
* mock py3dmol
* add note for pip installs
* fix quote
* temporarily resort to SettingsBaseModel to get build
* specific imports
* dont use base settings placeholder
* updating pins
* remove min 8.2 pin
* pin example notebooks version
* update branch
* a comma
* min of 8.1.1
* add comment about pydantic min
* adding comment for openff-units pin
* updating openmm pin
* draft for Konnektor integration
* changing back to mappers iterable as parameter
* consistently using Konnektor also in loading fep or orion net
* adding handles for Konnektor functionality.
* used black for formatting.
* Update test_network_planning.py
fix for tests
* fixes for unittests:
- fix removing the central ligand from list.
* Update test_network_planning.py
remove test for testing if a central component is part of the other component list. This can not happen anymore with the current Konnektor implementation, therefore I propose removing the test.
* updating docstrings
* adjusting n_processes docstring language
* fixing central_ligand default
* rename mappers to mapper to avoid api break
* Revert "rename mappers to mapper to avoid api break"
This reverts commit bf82085d7a86be63d2eaca11e105261107229ecc.
* fixing mapper/s to avoid api break
* switching arg names from 'ligands' to new 'components' keyword to match konnektor
* reverting ordering change
* fixing docstring
* pull konnektor from main for development only
* mapper back to mappers to avoid api break
* clean up
* formatting
* mapper->mappers
* fixing call to network_from_indices
* update radial network test scorer to return between 0 and 1
* organizing tests into classes
* expect only one mapping per edge for maximal networks
* adding TODOs
* adding TODOs for later
* update index error string to match konnektor's clarity improvement
* updating pytest.raises to look for RuntimeError instead of ValueError
* adding TODO
* making unreachable test clearer
* fixing regex AGAIN
* some light formatting
* cleaning up diff
* central_ligand -> central component for msg regex
* regex
* updating regexes to match new konnektor behavior
* formatting :(
* formatting :(
* add connectedness check
* updating TODO
* fix comment
* update progress bar docstring
* fix ambiguous var name
* remove unused imports
* fix mypy checks
* remove unused testing code
* pin konnektor to 0.2
* remove completed TODOs
* add konnektor to docs env
* remove completed TODO
* updating news
* clarifying process and progress additions in news
---------
Co-authored-by: Alyssa Travitz <atravitz@umich.edu>
Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io>
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
* updating git ignore and renaming to environment.yml for consistency
* bump to sphinx<7.3
* back to yaml
* test newset sphinx + install from cf
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
* use Lomap package's bindings
* fix mypy complaints
* Code via suggestions because local branch is borked
Why can't I push this from my local?
* Update openfe/setup/atom_mapping/lomap_scorers.py
* try exporting __all__ (make RTD happy too)
* guess mypy didn't like that at __all__
* Oh, *that* would be how to fix the warning about mocks
* Update environment.yaml
* Update environment.yml
* Update conf.py
* remove lomap docs
* try adding lomap to docs build
* try adding lomap scorer docs back
* add generate_lomap_network to docs
* Update environment.yml
---------
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io>
* mock everything we can and make the env as small as we can
* It 👏 is 👏 .yaml 👏 not 👏 .yml
* use a cache
* bump ci
* auto dist
* make warnings errors when building locally
